Variant report

Variant	nsv428743
Chromosome Location	chr3:89584946-89689096
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr3:89673701-89674049	HepG2	liver:	n/a	n/a
2	BATF	chr3:89681279-89681512	GM12878	blood:	n/a	n/a
3	BATF	chr3:89606556-89606723	GM12878	blood:	n/a	n/a
4	CEBPB	chr3:89627174-89627476	HepG2	liver:	n/a	n/a
5	CEBPB	chr3:89621439-89621799	IMR90	lung:	n/a	chr3:89621613-89621624
6	CEBPB	chr3:89611228-89611784	HepG2	liver:	n/a	chr3:89611652-89611663
7	CEBPB	chr3:89596888-89597213	A549	lung:	n/a	chr3:89597053-89597064 chr3:89597052-89597065
8	CEBPB	chr3:89688146-89688365	IMR90	lung:	n/a	chr3:89688223-89688234
9	CEBPB	chr3:89611477-89611841	H1-hESC	embryonic stem cell:	n/a	chr3:89611652-89611663
10	CEBPB	chr3:89596925-89597172	ECC-1	luminal epithelium:	n/a	chr3:89597053-89597064 chr3:89597052-89597065
11	CEBPB	chr3:89596919-89597179	IMR90	lung:	n/a	chr3:89597053-89597064 chr3:89597052-89597065
12	CEBPB	chr3:89684395-89684690	Hela-S3	cervix:	n/a	n/a
13	CEBPB	chr3:89621421-89621789	Hela-S3	cervix:	n/a	chr3:89621613-89621624
14	CEBPB	chr3:89633527-89633839	IMR90	lung:	n/a	chr3:89633669-89633682
15	CEBPB	chr3:89673160-89673467	HepG2	liver:	n/a	chr3:89673310-89673321 chr3:89673312-89673323 chr3:89673310-89673323 chr3:89673310-89673323
16	CEBPB	chr3:89684350-89684696	IMR90	lung:	n/a	n/a
17	CEBPB	chr3:89596891-89597236	HepG2	liver:	n/a	chr3:89597053-89597064 chr3:89597052-89597065
18	CEBPB	chr3:89612444-89612618	H1-hESC	embryonic stem cell:	n/a	n/a
19	CEBPB	chr3:89684505-89684527	H1-hESC	embryonic stem cell:	n/a	n/a
20	CEBPB	chr3:89621462-89621736	HepG2	liver:	n/a	chr3:89621613-89621624
21	CEBPB	chr3:89677575-89677724	A549	lung:	n/a	chr3:89677682-89677695
22	CEBPB	chr3:89671217-89671525	HepG2	liver:	n/a	chr3:89671346-89671357
23	CEBPB	chr3:89627476-89627616	H1-hESC	embryonic stem cell:	n/a	n/a
24	CEBPB	chr3:89596934-89597217	Hela-S3	cervix:	n/a	chr3:89597053-89597064 chr3:89597052-89597065
25	CEBPB	chr3:89621497-89621748	A549	lung:	n/a	chr3:89621613-89621624
26	CEBPB	chr3:89688131-89688356	HepG2	liver:	n/a	chr3:89688223-89688234
27	CEBPB	chr3:89609784-89610154	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr3:89611669-89611756	LNCaP	prostate:	n/a	n/a
29	CTCF	chr3:89611640-89611790	HRPEpiC	eye:	n/a	n/a
30	CTCF	chr3:89611641-89611765	HepG2	liver:	n/a	n/a
31	CTCF	chr3:89611560-89611710	MCF-7	breast:	n/a	n/a
32	CTCF	chr3:89635940-89636090	MCF-7	breast:	n/a	n/a
33	CTCF	chr3:89611620-89611789	LNCaP	prostate:	n/a	n/a
34	CTCF	chr3:89611640-89611790	HCPEpiC	choroid plexus:	n/a	n/a
35	CTCF	chr3:89635960-89636110	HMEC	breast:	n/a	n/a
36	CTCF	chr3:89611580-89611730	HepG2	liver:	n/a	n/a
37	CTCF	chr3:89611535-89611844	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr3:89636002-89636117	GM20000	blood:	n/a	n/a
39	CTCF	chr3:89611620-89611770	SK-N-SH_RA	brain:	n/a	n/a
40	CTCF	chr3:89611541-89611875	GM12878	blood:	n/a	n/a
41	CTCF	chr3:89599879-89599922	GM13976	blood:	n/a	n/a
42	CTCF	chr3:89611519-89611875	MCF-7	breast:	n/a	n/a
43	CTCF	chr3:89611680-89611830	HCPEpiC	choroid plexus:	n/a	n/a
44	CTCF	chr3:89611720-89611870	HCFaa	heart:	n/a	n/a
45	CTCF	chr3:89666920-89667070	AG09319	gingival:	n/a	n/a
46	CTCF	chr3:89611660-89611810	NHLF	lung:	n/a	n/a
47	CTCF	chr3:89611674-89611805	HepG2	liver:	n/a	n/a
48	CTCF	chr3:89611600-89611750	HRE	kidney:	n/a	n/a
49	CTCF	chr3:89594680-89594830	Caco-2	colon:	n/a	n/a
50	CTCF	chr3:89635996-89636134	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:89606382..89608031-chr3:89610038..89611575,2	MCF-7	breast:
2	chr3:89648727..89651109-chr3:89653242..89655047,2	MCF-7	breast:
3	chr3:89586920..89589016-chr3:89591603..89593114,2	MCF-7	breast:
4	chr3:89611023..89612234-chr3:89900845..89901820,5	MCF-7	breast:
5	chr3:89586920..89589016-chr3:89591603..89593114,2	MCF-7	breast:
6	chr3:89645876..89647847-chr3:89649873..89652502,3	MCF-7	breast:
7	chr3:89611242..89611987-chr3:90140381..90141293,2	MCF-7	breast:
8	chr3:89606382..89608031-chr3:89610038..89611575,2	MCF-7	breast:
9	chr3:89648727..89651109-chr3:89653242..89655047,2	MCF-7	breast:
10	chr3:89645876..89647847-chr3:89649873..89652502,3	MCF-7	breast:
11	chr1:11968828..11971360-chr3:89649996..89651496,2	K562	blood:

Variant related genes	Relation type
ENSG00000240951	TF binding region
ENSG00000240309	TF binding region
ENSG00000201801	chromatin interactions

Extended variants
information (count: 2060 )
Associated
traits (count: 79 )

Variant overlapped rSNPs/rCNVs (count:2060 , 50 per page) page: 1 2 3 4 5 6 7 ... 42

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs567218600	chr3:89595670-89595671	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs578049272	chr3:89595734-89595735	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs187529619	chr3:89595776-89595777	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs558894772	chr3:89595798-89595799	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs577231241	chr3:89595799-89595800	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs116234077	chr3:89595809-89595810	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs374877692	chr3:89595813-89595814	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs556644071	chr3:89595869-89595870	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs545241654	chr3:89595936-89595937	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs559721880	chr3:89595937-89595938	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs138181164	chr3:89595946-89595947	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs79782314	chr3:89595951-89595952	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs34354304	chr3:89595976-89595977	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs545561785	chr3:89596004-89596005	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs207463305	chr3:89596027-89596028	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs192642897	chr3:89596028-89596029	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs375278439	chr3:89596038-89596039	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs141322158	chr3:89596056-89596057	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs531565463	chr3:89596094-89596095	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs529483607	chr3:89598206-89598207	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs547478845	chr3:89598222-89598223	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs7625792	chr3:89598252-89598253	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs184582400	chr3:89598260-89598261	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs558143351	chr3:89598310-89598311	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs57038551	chr3:89598353-89598354	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs398106162	chr3:89598354-89598355	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs569817525	chr3:89598367-89598368	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs578006916	chr3:89598369-89598370	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs537373436	chr3:89598387-89598388	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs555728051	chr3:89598425-89598426	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs539157392	chr3:89598436-89598437	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs140893482	chr3:89598493-89598494	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs528644800	chr3:89598540-89598541	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs189108938	chr3:89598546-89598547	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs144837831	chr3:89598579-89598580	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs181969292	chr3:89598607-89598608	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs577668267	chr3:89598664-89598665	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs186341121	chr3:89598694-89598695	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs73145345	chr3:89598696-89598697	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs563320524	chr3:89598700-89598701	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs530452857	chr3:89598707-89598708	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs56012803	chr3:89598748-89598749	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs189080789	chr3:89598760-89598761	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs562086392	chr3:89598792-89598793	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs529443838	chr3:89598822-89598823	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs547588164	chr3:89598833-89598834	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs181732984	chr3:89598836-89598837	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs145843291	chr3:89598857-89598858	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs75613479	chr3:89598890-89598891	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs34292386	chr3:89598896-89598897	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:79)

Disease	PMID	Source
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Acute myeloid leukemia	20729466	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Metanephric adenoma	20802469	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Soft tissue tumor	16732325	CNVD
Neurodevelopmental disorder	22521361	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
craniofacial dysmorphism	21918468	CNVD
Cancer	20164920	CNVD
Lung cancer	19547694	CNVD
Cancer	20164919	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Melanoma	20877625	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
small cell lung cancer	20016488	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Bipolar disorder	19114987	CNVD

Chromatin state (count:137 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89595600-89596000	Enhancers	Ovary	ovary
2	chr3:89595800-89596200	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr3:89595800-89596200	Enhancers	Brain Substantia Nigra	brain
4	chr3:89598200-89599000	Enhancers	Fetal Heart	heart
5	chr3:89606000-89606200	Enhancers	HMEC	breast
6	chr3:89607600-89608800	Enhancers	Ovary	ovary
7	chr3:89608400-89609600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:89608400-89610600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr3:89608600-89609600	Enhancers	Placenta Amnion	Placenta Amnion
10	chr3:89608600-89610400	Enhancers	Fetal Heart	heart
11	chr3:89608600-89610600	Enhancers	HMEC	breast
12	chr3:89609400-89610000	Enhancers	HSMMtube	muscle
13	chr3:89610200-89610800	Active TSS	Aorta	Aorta
14	chr3:89610600-89613000	Weak transcription	HMEC	breast
15	chr3:89610800-89613200	Weak transcription	Aorta	Aorta
16	chr3:89613000-89614800	Enhancers	HMEC	breast
17	chr3:89613200-89614400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:89613800-89614200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:89614000-89614600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:89614000-89614800	Enhancers	NH-A	brain
21	chr3:89618000-89621200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:89618200-89620400	Weak transcription	Spleen	Spleen
23	chr3:89619400-89620200	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:89619400-89620200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr3:89619600-89620000	Enhancers	Psoas Muscle	Psoas
26	chr3:89619600-89620200	Enhancers	Brain Hippocampus Middle	brain
27	chr3:89619600-89620400	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr3:89619600-89620400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr3:89619600-89620800	Enhancers	Stomach Smooth Muscle	stomach
30	chr3:89619600-89621200	Enhancers	Brain Cingulate Gyrus	brain
31	chr3:89619600-89621200	Enhancers	Fetal Muscle Leg	muscle
32	chr3:89619600-89621400	Enhancers	Brain Angular Gyrus	brain
33	chr3:89619600-89621400	Enhancers	Ovary	ovary
34	chr3:89619800-89620200	Enhancers	Brain Substantia Nigra	brain
35	chr3:89619800-89621400	Enhancers	Fetal Muscle Trunk	muscle
36	chr3:89620000-89620400	Weak transcription	Psoas Muscle	Psoas
37	chr3:89620200-89620400	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr3:89620200-89620600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:89620200-89621000	Flanking Active TSS	Brain Hippocampus Middle	brain
40	chr3:89620200-89621000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:89620200-89621000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr3:89620200-89621400	Enhancers	Brain Anterior Caudate	brain
43	chr3:89620200-89621400	Enhancers	Fetal Stomach	stomach
44	chr3:89620200-89621600	Enhancers	Fetal Heart	heart
45	chr3:89620400-89620600	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr3:89620400-89620600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr3:89620400-89621000	Active TSS	Brain Substantia Nigra	brain
48	chr3:89620400-89621000	Enhancers	Spleen	Spleen
49	chr3:89620400-89621200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr3:89620400-89621200	Enhancers	Fetal Lung	lung

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